Changes between Version 8 and Version 9 of DataManagement/SftpServer


Ignore:
Timestamp:
Aug 18, 2011 9:31:19 PM (13 years ago)
Author:
laurent
Comment:

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  • DataManagement/SftpServer

    v8 v9  
    2222
    2323=== personal users ===
    24 
    25 ==== /target/gpfs2/gcc/groups/gonl/ ====
    26 Root of the gonl data.
    27 
    28 ==== /target/gpfs2/gcc/groups/gonl/projects ====
    29 Root of the gonl projects. This is where all the raw data and results live. They are organized into projects; please have a look at the full data structure here: DataManagement/ProjectData
    30 ==== /target/gpfs2/gcc/groups/gonl/projects/bgi ====
    31 Contains all the data coming from BGI, including their variant calls.  The data is organized by batch in the batchX subfolders. Each of the  subfolders typically contains the following:
    32 
    33  * batchX/
    34    * A  set of compressed files containing the plain text data and md5 files  for downloading purpose. These are named as follows:  timestamp.BGI.batchX.data_type.hg1X.data_format.tar.bz2. All plain text  data should be available as a compressed file, including but not limited  to: CNV, !InDel, !InDel annotations, SNP, SNP annotation. Some of these  are available in multiple formats; see BGI data page for more  explanation about the BGI data and its formats. ** md5 checksum files  for all files.
    35 
    36  * batchX/bam OR batchX/alignment
    37    * The BAM files aligned by BGI
    38 
    39  * batchX/CNV
    40    * CNVs in CNV Detector format. If you want to download for all samples, please download the compressed archive from batchX/
    41 
    42  * batchX/indel
    43    * !InDels in samtools pileup format. If you want to download for all samples, please download the compressed archive from batchX/
    44 
    45  * batchX/indel_annotation
    46    * Indels annotations in GFF format. If you want to download for all samples, please download the compressed archive from batchX/
    47 
    48  * batchX/SNP
    49    * SNP in SOAPsnp format. If you want to download for all samples, please download the compressed archive from batchX/
    50 
    51  * batchX/SNP_annotation
    52    * SNP annotations in GFF format. If you want to download for all samples, please download the compressed archive from batchX/
    53 
    54  * batchX/vcf_format/CNV
    55    * CNV in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
    56 
    57  * batchX/vcf_format/indel
    58    * Indel in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
    59 
    60  * batchX/vcf_format/SNP
    61    * SNP in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
    62 
    63 NOTES:
    64 
    65  * Unless specified otherwise, all data is aligned on hg19
    66  * Some  of the folder/filenames are inconsistent from one batch to the other.  This is because the original names as found on the BGI HD have been  kept.
     24Personal users should refer to this page for the description of the folder structure holding the data: !DataManagement/ProjectData